Publications

characterization of bsemii, a new type iv restriction-modification system, which recognizes the pentanucleotide sequence 5'-ctcag(n)(10/8)/.	we report the properties of the new bsemii restriction and modification enzymes from bacillus stearothermophilus isl 15-111, which recognize the 5'-ctcag sequence, and the nucleotide sequence of the genes encoding them. the restriction endonuclease r.bsemii makes a staggered cut at the tenth base pair downstream of the recognition sequence on the upper strand, producing a two base 3'-protruding end. magnesium ions and s:-adenosyl-l-methionine (adomet) are required for cleavage. s:-adenosylhomocy ...	2001	11160921
catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and x-ray crystallographic investigation.	the catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (mdh) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (pqq). a crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. a theoretical an ...	2001	11149955
urea utilization in the phototrophic bacterium rhodobacter capsulatus is regulated by the transcriptional activator ntrc.	the phototrophic nonsulfur purple bacterium rhodobacter capsulatus can use urea as a sole source of nitrogen. three transposon tn5-induced mutations (xan-9, xan-10, and xan-19), which led to a ure(-) phenotype, were mapped to the uref and urec genes, whereas two other tn5 insertions (xan-20 and xan-22) were located within the ntrc and ntrb genes, respectively. as in klebsiella aerogenes and other bacteria, the genes encoding urease (ureabc) and the genes required for assembly of the nickel metal ...	2001	11133958
chloromethane utilization gene cluster from hyphomicrobium chloromethanicum strain cm2(t) and development of functional gene probes to detect halomethane-degrading bacteria.	hyphomicrobium chloromethanicum cm2(t), an aerobic methylotrophic member of the alpha subclass of the class proteobacteria, can grow with chloromethane as the sole carbon and energy source. h. chloromethanicum possesses an inducible enzyme system for utilization of chloromethane, in which two polypeptides (67-kda cmua and 35-kda cmub) are expressed. previously, four genes, cmua, cmub, cmuc, and puru, were shown to be essential for growth of methylobacterium chloromethanicum on chloromethane. the ...	2001	11133460
effect of model sorptive phases on phenanthrene biodegradation: molecular analysis of enrichments and isolates suggests selection based on bioavailability.	reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. we established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (r. j. grosser, m. friedrich, d. m. ward, and w. p. inskeep, appl. environ. microbiol. 66:2695-2702, 2000). bacteria enriched and isolated from contaminated soils under these conditions were ...	2000	10877758
prokaryotic diversity in zostera noltii-colonized marine sediments.	the diversity of microorganisms present in a sediment colonized by the phanerogam zostera noltii has been analyzed. microbial dna was extracted and used for constructing two 16s rdna clone libraries for bacteria and archaea. bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. eight major lineages of the domain bacteria were represented in the library. the most frequently retrieved bacterial group (36% of the clones) was delta- ...	2000	10742267
identification by genetic suppression of escherichia coli tolb residues important for tolb-pal interaction.	the tol-pal system of escherichia coli is involved in maintaining outer membrane stability. mutations in tolq, tolr, tola, tolb, or pal genes result in sensitivity to bile salts and the leakage of periplasmic proteins. moreover, some of the tol genes are necessary for the entry of group a colicins and the dna of filamentous bacteriophages. tolq, tolr, and tola are located in the cytoplasmic membrane where they interact with each other via their transmembrane domains. tolb and pal form a periplas ...	2000	10633120
the mitochondrial alcohol dehydrogenase adh3p is involved in a redox shuttle in saccharomyces cerevisiae.	ndi1 is the unique gene encoding the internal mitochondrial nadh dehydrogenase of saccharomyces cerevisiae. the enzyme catalyzes the transfer of electrons from intramitochondrial nadh to ubiquinone. surprisingly, ndi1 is not essential for respiratory growth. here we demonstrate that this is due to in vivo activity of an ethanol-acetaldehyde redox shuttle, which transfers the redox equivalents from the mitochondria to the cytosol. cytosolic nadh can be oxidized by the external nadh dehydrogenases ...	2000	10940011
comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria.	in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ...	2000	11055963
distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases.	the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ...	1999	10482517
localization of periplasmic redox proteins of alcaligenes faecalis by a modified general method for fractionating gram-negative bacteria.	a lysozyme-osmotic shock method is described for fractionation of alcaligenes faecalis which uses glucose to adjust osmotic strength and multiple osmotic shocks. during phenylethylamine-dependent growth, aromatic amine dehydrogenase, azurin, and a single cytochrome c were localized in the periplasm. their induction patterns are different from those for the related quinoprotein methylamine dehydrogenase and its associated redox proteins.	1999	10515948
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.	paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...	1998	9841665
physical, biochemical, and immunological characterization of a thermostable amidase from klebsiella pneumoniae nctr 1.	an amidase capable of degrading acrylamide and aliphatic amides was purified to apparent homogeneity from klebsiella pneumoniae nctr 1. the enzyme is a monomer with an apparent molecular weight of 62,000. the ph and temperature optima of the enzyme were 7.0 and 65 degrees c, respectively. the purified amidase contained 11 5,5-dithiobis(2-nitrobenzoate) (dtnb)-titratable sulfhydryl (sh) groups. in the native enzyme 1.0 sh group readily reacted with dtnb with no detectable loss of activity. titrat ...	1996	8636044
three-dimensional structure of human electron transfer flavoprotein to 2.1-a resolution.	mammalian electron transfer flavoproteins (etf) are heterodimers containing a single equivalent of flavin adenine dinucleotide (fad). they function as electron shuttles between primary flavoprotein dehydrogenases involved in mitochondrial fatty acid and amino acid catabolism and the membrane-bound electron transfer flavoprotein ubiquinone oxidoreductase. the structure of human etf solved to 2.1-a resolution reveals that the etf molecule is comprised of three distinct domains: two domains are con ...	1996	8962055
improved large scale culture of methylophilus methylotrophus for 13c/15n labeling and random fractional deuteration of ribonucleotides.	isotopic labeling of rna with 13c and 15n has become a routine procedure in structural studies by nmr spectroscopy. the methodology in this paper describes the random fractional deuteration of rna using the obligate methylotropic bacterium, methylophilus methylotrophus. this bacterium was grown using a non-deuterated carbon source in 52:48 d20/h20 and we have shown that all protons in the ribonucleotides except for the ribose h1 become 52% randomly fractionally deuterated. improved growth condit ...	1996	8972874
cloning, sequencing, and mutation of a gene for azurin in methylobacillus flagellatum kt.	the gene cluster for methylamine utilization (mau genes) has been cloned from the obligate methylotrophic bacterium methylobacillus flagellatum kt. partial sequence data showed that the organization of these genes was similar to that found in methylophilus methylotrophus w3a1-ns, including the lack of a gene for amicyanin, which had been thought to be the electron acceptor for methylamine dehydrogenase in m. flagellatum kt. however, a gene encoding azurin was discovered at the 3' end of the mau ...	1995	7635847
the reca protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of recas and 16s rrnas from the same species.	the evolution of the reca protein was analyzed using molecular phylogenetic techniques. phylogenetic trees of all currently available complete reca proteins were inferred using multiple maximum parsimony and distance matrix methods. comparison and analysis of the trees reveal that the inferred relationships among these proteins are highly robust. the reca trees show consistent subdivisions corresponding to many of the major bacterial groups found in trees of other molecules including the alpha, ...	1995	8587109
organization of the methylamine utilization (mau) genes in methylophilus methylotrophus w3a1-ns.	the organization of genes involved in utilization of methylamine (mau genes) was studied in methylophilus methylotrophus w3a1. the strain used was a nonmucoid variant termed ns (nonslimy). the original mucoid strain was shown to be identical to the ns strains on the basis of chromosomal digest and hybridization patterns. an 8-kb psti fragment of the chromosome from m. methylotrophus w3a1-ns encoding the mau genes was cloned and a 6,533-bp region was sequenced. eight open reading frames were foun ...	1994	8021188
genetic organization of the mau gene cluster in methylobacterium extorquens am1: complete nucleotide sequence and generation and characteristics of mau mutants.	the nucleotide sequence of the methylamine utilization (mau) gene region from methylobacterium extorquens am1 was determined. open reading frames for 11 genes (maufbedacjglmn) were found, all transcribed in the same orientation. the maub, maua, and mauc genes encode the periplasmic methylamine dehydrogenase (madh) large and small subunit polypeptides and amicyanin, respectively. the products of maud, maug, maul, and maum were also predicted to be periplasmic. the products of mauf, maue, and maun ...	1994	8021187
preparation of isotopically labeled ribonucleotides for multidimensional nmr spectroscopy of rna.	a general method for large scale preparation of uniformly isotopically labeled ribonucleotides and rnas is described. bacteria are grown on isotopic growth medium, and their nucleic acids are harvested and degraded to mononucleotides. these are enzymatically converted into ribonucleoside triphosphates, which are used in transcription reactions in vitro to prepare rnas for nmr studies. for 15n-labeling, e.coli is grown on 15n-ammonium sulfate, whereas for 13c-labeling, methylophilus methylotrophu ...	1992	1383928
characterization of mutant forms of the quinoprotein methanol dehydrogenase lacking an essential calcium ion.	methanol dehydrogenase (mdh) from methylobacterium extorquens, methylophilus methylotrophus, paracoccus denitrificans and hyphomicrobium x all contained a single atom of ca2+ per alpha 2 beta 2 tetramer. the role of ca2+ was investigated using the mdh from methylobacterium extorquens. this was shown to be similar to the mdh from hyphomicrobium x in having 2 mol of prosthetic group (pyrroloquinoline quinine; pqq) per mol of tetramer, the pqq being predominantly in the semiquinone form. mdh isolat ...	1992	1332681
cytochrome c'' isolated from methylophilus methylotrophus. an example of bis-histidine-co-ordinated fe3+ haem, with near-perpendicular orientation of the ligands.	cytochrome c'' (methylophilus methylotrophus) is a soluble protein, mr 15,000, possessing one haem which is high-spin in the reduced state but switches to a low-spin form on oxidation. low-temperature electron-paramagnetic-resonance spectroscopy of the oxidized state shows a low-spin signal at gz = 3.65 with a folded line-shape typical of a haem of low rhombicity, and the near-infrared magnetic-circular-dichroism (m.c.d.) spectra reveal an unusually intense (delta epsilon = 400 m-1.cm-1 at 5 t, ...	1990	2169241
studies on electron transfer from methanol dehydrogenase to cytochrome cl, both purified from hyphomicrobium x.	ferricytochrome cl isolated from hyphomicrobium x is an electron acceptor in assays for homologous methanol dehydrogenase (mdh), albeit a poor one compared with artificial dyes. the intermediates of mdh seen during the reaction are identical with those observed with wurster's blue as electron acceptor, indicating that the reaction cycles are similar. the assay showed a ph optimum of approx. 7.0 and scarcely any stimulation by nh4cl, this being in contrast with assays with artificial dyes, where ...	1989	2537627
isolation of auxotrophic mutants of methylophilus methylotrophus by modified-marker exchange.	a method for stabilizing a transposon (tn5) has been developed which allows the isolation of stable auxotrophic mutants of methylophilus methylotrophus asi. insertion of tn5 into a cloned m. methylotrophus asi dna fragment encoding anthranilate synthase followed by transfer of the vector with the modified trpe gene to m. methylotrophus asi resulted in unstable auxotrophs among the recombinants. deletion of is50r, which encodes transposase production from tn5, stabilized the transposon after mobi ...	1988	16347531
electron transfer flavoprotein from methylophilus methylotrophus: properties, comparison with other electron transfer flavoproteins, and regulation of expression by carbon source.	when grown on methylated amines as a carbon source, methylophilus methylotrophus synthesizes an electron transfer flavoprotein (etf) which is the natural electron acceptor of trimethylamine dehydrogenase. it is composed of two dissimilar subunits of 38,000 and 42,000 daltons and 1 mol of flavin adenine dinucleotide. it was reduced by trimethylamine dehydrogenase to a stable anionic semiquinone form, which could not be converted, either enzymatically or chemically, to the fully reduced dihydroqui ...	1986	3711024
isolation and computer-aided characterization of mmei, a type ii restriction endonuclease from methylophilus methylotrophus.	a type ii restriction endonuclease, mmei, has been purified from the obligate methylotroph, methylophilus methylotrophus. the enzyme was shown to have the non-palindromic recognition sequence 5'-t c c pu a c (n)20-3', 3'-a g g py t g (n)18-5' and to cleave (as indicated) on the 3' side, generating a two nucleotide 3' projection. determination of the recognition sequence was achieved using two new computer programs; recog, which predicts recognition sequences from the pattern of restriction fragm ...	1986	3016643
expression of a chemically synthesized human alpha 1 interferon gene.	cells of escherichia coli containing a chemically synthesized human alpha 1 interferon (ifn-alpha 1) gene, under control of the lac promoter, make a product with biological properties indistinguishable from those of the natural ifn-alpha 1 [antiviral activity, acid stability, species crossreactivity, inactivation by antisera directed against leukocyte or namalwa cell interferon, and stimulation of (2'-5')oligoadenylate synthetase activity]. similar levels of ifn synthesis were obtained when the ...	1982	6181502
the autoreducible cytochromes c of the methylotrophs methylophilus methylotrophus and pseudomonas am1.	the two types of soluble cytochrome c (cytochrome ch and cytochrome cl) found in methylotrophs are completely distinct proteins; one type is not a dimer or degradation product of the other. free thiol groups are probably not involved in the unusually rapid autoreduction of the cytochromes at high ph. the axial ligands to the haem iron, histidine and methionine, are the same as in other low-spin cytochromes c. the methionine ligand is displaced at high ph by an alternative strong-field ligand. th ...	1982	6295363
purification and properties of the methanol dehydrogenase from methylophilus methylotrophus.	1. a dye-linked methanol dehydrogenase, resembling many others from a variety of methylotrophic bacteria, was purified to homogeneity from extracts of methanol-grown methylophilus methylotrophus. 2. the enzyme was very stable in the presence of methanol; in the absence of methanol it had a half-life of 1-2 days at 4 degrees c. 3. the value of a1% 1cm,280 was 17.5. 4. the enzyme retained bound methanol after passage through sephadex g-25. this tightly-bound methanol slowly exchanged with free [14 ...	1981	6802134
respiration-linked proton translocation in the obligate methylotroph methylophilus methylotrophus.	the stoicheiometries of respiration-linked proton translocation in methylophilus methylotrophus were determined by using both the oxygen-pulse and initial-rate methods. the latter has also been used to determine leads to charge/o quotients (measured as yield k+/o quotients) in order to ascertain whether the leads to h+/o quotients might be underestimated by h+/anion symport. the results suggest that 6h+/o are translocated during nadh oxidation, and that 2h+/o are translocated during the oxidatio ...	1981	6272739
the purification and properties of the soluble cytochromes c of the obligate methylotroph methylophilus methylotrophus.	the obligate methylotroph methylophilus methylotrophus contains three distinct soluble cytochromes c. the major cytochromes, cytochrome ch (about 50% of the total) and cytochrome cl (about 42%), were similar in most respects to the cytochromes ch and cl of the facultative methylotroph pseudomonas am1 [o'keeffe & anthony (1980) biochem. j. 192, 411-419]. cytochrome ch had a high isoelectric point, a midpoint redox potential at ph 7.0 of 373 mv and a low molecular weight (8500). the cytochrome cl ...	1980	6263254
the electron-transport chains of the obligate methylotroph methylophilus methylotrophus.	the cytochrome complement of methylophilus methylotrophus and its respiratory properties were determined during batch culture and in continuous culture under conditions of methanol-, nitrogen- and o(2)-limitation. about 35% of the cytochrome c produced by the bacteria was released into the growth medium, and of the remaining cytochrome c about half was membrane-bound and half was soluble. two cytochromes c were always present on membranes (redox potentials 375mv and 310mv), and these probably co ...	1980	7236221